Over 30,000 faithful gathered at the capital's central square for the first ever beatification ceremony held in Lithuania.
Lithuanian President Dalia Grybauskaitė, Prime Minister Saulius Skvernelis and Viktoras Pranckietis, the speaker of the Seimas, were among those who attended Sunday's beatification mass led by Cardinal Angelo Amato.
In his Apostolic Letter of Beatification, read by the Vatican's representative, Pope Francis called Matulionis "a shepherd according to the heart of Christ, a heroic witness to the Gospel, a courageous defender of the Church and of human dignity".
Matulionis spent 16 years in Soviet prisons and forced labor camps. The priest in 1946 received his longest prison sentence for refusing to cooperate with the Soviet regime in fighting Lithuania's armed anti-Soviet resistance and for criticizing the Communist Party for its repression of the faithful.
After spending 10 years in prison, Matulionis was allowed to return to the Soviet-occupied Lithuania and secretly consecrated Vincentas Sladkevičius as bishop.
Matulionis died in 1962 at the age of 89. It is suspected that he was poisoned by the secret KGB police, but this has not been proved.
Addressing the crowd, Cardinal Angelo Amato said that the privations and tortures had not bent Matulionis' will.
"The hostility of the Nazis and the communists had no rational basis. It was merely the fruit of their hatred toward the Gospel of Jesus and the Church," the Vatican's representative said in his homily.
"The new Blessed faced this stormy sea with peace and strength of mind, remaining always firm in the faith and the hope of future liberation. He did not give in to hatred. For him, hating would have been the worst way to answer evil. His response was always to forgive," he said.
Matulionis is the second Blessed of Lithuania. Bishop Jurgis Matulaitis was beatified in Rome in 1987.
For Matulionis to be canonized as a saint, a miracle has to be attributed to his intercession.
Lithuania has one patron saint -- Saint Casimir Jagiellon, a prince of the Grand Duchy of Lithuania and the Kingdom of Poland who lived in the 15th century and was canonized in 1602.